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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 2-69329679-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=69329679&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 69329679,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000357308.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1597+5A>G",
"hgvs_p": null,
"transcript": "NM_001244710.2",
"protein_id": "NP_001231639.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 699,
"cds_start": -4,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8665,
"mane_select": "ENST00000357308.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1597+5A>G",
"hgvs_p": null,
"transcript": "ENST00000357308.9",
"protein_id": "ENSP00000349860.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 699,
"cds_start": -4,
"cds_end": null,
"cds_length": 2100,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8665,
"mane_select": "NM_001244710.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1543+5A>G",
"hgvs_p": null,
"transcript": "ENST00000361060.5",
"protein_id": "ENSP00000354347.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 681,
"cds_start": -4,
"cds_end": null,
"cds_length": 2046,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1543+5A>G",
"hgvs_p": null,
"transcript": "NM_002056.4",
"protein_id": "NP_002047.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 681,
"cds_start": -4,
"cds_end": null,
"cds_length": 2046,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1543+5A>G",
"hgvs_p": null,
"transcript": "ENST00000674507.1",
"protein_id": "ENSP00000501332.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 625,
"cds_start": -4,
"cds_end": null,
"cds_length": 1878,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1327+5A>G",
"hgvs_p": null,
"transcript": "ENST00000674438.1",
"protein_id": "ENSP00000501469.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 609,
"cds_start": -4,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1672+5A>G",
"hgvs_p": null,
"transcript": "XM_017003801.2",
"protein_id": "XP_016859290.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 724,
"cds_start": -4,
"cds_end": null,
"cds_length": 2175,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8662,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"hgvs_c": "c.1618+5A>G",
"hgvs_p": null,
"transcript": "XM_017003802.3",
"protein_id": "XP_016859291.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 706,
"cds_start": -4,
"cds_end": null,
"cds_length": 2121,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GFPT1",
"gene_hgnc_id": 4241,
"dbsnp": "rs373420002",
"frequency_reference_population": 0.000057464007,
"hom_count_reference_population": 1,
"allele_count_reference_population": 91,
"gnomad_exomes_af": 0.0000537978,
"gnomad_genomes_af": 0.0000919142,
"gnomad_exomes_ac": 77,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7400000095367432,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.08399999886751175,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.181,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000669287774174198,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000357308.9",
"gene_symbol": "GFPT1",
"hgnc_id": 4241,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1597+5A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital myasthenic syndrome 12,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Congenital myasthenic syndrome 12|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}